alt Hacker Newsslighlty disagree with this. A fixed page layout has it's own advantages. The reason we have more high quality pdf readers than epub readers is probrably connected to the format itself. PDF readers usally are more more feature complete when it comes to stuff like annotations too.
My issue with EPUB readers is about features a PDF reader wouldn't even have. Small and annoying things like how much freedom I get when changing fonts and whatnot.
I haven't had a need to use annotations. I guess that could be solved by EPUB editors, but I haven't tested any, apart from any text editors after unzipping the EPUB.